#include <parm.h>

Public Member Functions
	parm ()

	~parm ()

FILE *	genopen (const char *name)

void	genclose (FILE *)

char *	get (int)

void	preadln (FILE , const char , char *)

int	readparm (char *)

int	firstwat ()

int	read_fortran_12I6 (FILE , int , int)

int	moveto (FILE , const char )

Public Attributes
char	ititl [81]

int	IfBox

int	Nmxrs

int	IfCap

int	Natom

int	Ntypes

int	Nbonh

int	Mbona

int	Ntheth

int	Mtheta

int	Nphih

int	Mphia

int	Nhparm

int	Nparm

int	Nnb

int	Nres

int	Nbona

int	Ntheta

int	Nphia

int	Numbnd

int	Numang

int	Nptra

int	Natyp

int	Nphb

int	Nat3

int	Ntype2d

int	Nttyp

int	Nspm

int	Iptres

int	Nspsol

int	Ipatm

int	Natcap

char *	AtomNames

char *	ResNames

char *	AtomSym

char *	AtomTree

_REAL *	Charges

_REAL *	Masses

_REAL *	Rk

_REAL *	Req

_REAL *	Tk

_REAL *	Teq

_REAL *	Pk

_REAL *	Pn

_REAL *	Phase

_REAL *	Solty

_REAL *	Cn1

_REAL *	Cn2

_REAL *	HB12

_REAL *	HB6

_REAL	Box [3]

_REAL	Cutcap

_REAL	Xcap

_REAL	Ycap

_REAL	Zcap

int *	Iac

int *	Iblo

int *	Cno

int *	Ipres

int *	ExclAt

int *	TreeJoin

int *	AtomRes

int *	BondHAt1

int *	BondHAt2

int *	BondHNum

int *	BondAt1

int *	BondAt2

int *	BondNum

int *	AngleHAt1

int *	AngleHAt2

int *	AngleHAt3

int *	AngleHNum

int *	AngleAt1

int *	AngleAt2

int *	AngleAt3

int *	AngleNum

int *	DihHAt1

int *	DihHAt2

int *	DihHAt3

int *	DihHAt4

int *	DihHNum

int *	DihAt1

int *	DihAt2

int *	DihAt3

int *	DihAt4

int *	DihNum

int *	Boundary

int	popn

int	data_read

Detailed Description

Definition at line 15 of file parm.h.

Constructor & Destructor Documentation

Ambertoppar::parm ( )

Definition at line 1124 of file parm.C.

References AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Boundary, Charges, Cn1, Cn2, Cno, data_read, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, ExclAt, HB12, HB6, Iac, Iblo, Ipres, Masses, Phase, Pk, Pn, Req, ResNames, Rk, Solty, Teq, Tk, and TreeJoin.

 {
   data_read = 0;        // No data are read yet
   AtomNames = ResNames = AtomSym = AtomTree = NULL;
   Charges = Masses = Rk = Req = Tk = Teq = Pk = Pn = Phase = NULL;
   Solty = Cn1 = Cn2 = HB12 = HB6 = NULL;
   Iac = Iblo = Cno = Ipres = ExclAt = TreeJoin = AtomRes = NULL;
   BondHAt1 = BondHAt2 = BondHNum = BondAt1 = BondAt2 = NULL;
   BondNum = AngleHAt1 = AngleHAt2 = AngleHAt3 = AngleHNum = NULL;
   AngleAt1 = AngleAt2 = AngleAt3 = AngleNum = DihHAt1 = NULL;
   DihHAt2 = DihHAt3 = DihHAt4 = DihHNum = DihAt1 = DihAt2 = NULL;
   DihAt3 = DihAt4 = DihNum = Boundary = NULL;
 }

Ambertoppar::~parm ( )

Definition at line 1141 of file parm.C.

References AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Charges, Cn1, Cn2, Cno, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, ExclAt, HB12, HB6, Iac, Iblo, Ipres, Masses, Phase, Pk, Pn, Req, ResNames, Rk, Solty, Teq, Tk, and TreeJoin.

 {
   free(AtomNames);
   free(Charges);
   free(Masses);
   free(Iac);
   free(Iblo);
   free(Cno);
   free(ResNames);
   free(Ipres);
   free(Rk);
   free(Req);
   free(Tk);
   free(Teq);
   free(Pk);
   free(Pn);
   free(Phase);
   free(Solty);
   free(Cn1);
   free(Cn2);
   free(BondHAt1);
   free(BondHAt2);
   free(BondHNum);
   free(BondAt1);
   free(BondAt2);
   free(BondNum);
   free(AngleHAt1);
   free(AngleHAt2);
   free(AngleHAt3);
   free(AngleHNum);
   free(AngleAt1);
   free(AngleAt2);
   free(AngleAt3);
   free(AngleNum);
   free(DihHAt1);
   free(DihHAt2);
   free(DihHAt3);
   free(DihHAt4);
   free(DihHNum);
   free(DihAt1);
   free(DihAt2);
   free(DihAt3);
   free(DihAt4);
   free(DihNum);
   free(ExclAt);
   free(HB12);
   free(HB6);
   free(AtomSym);
   free(AtomTree);
   free(TreeJoin);
   free(AtomRes);
 }

Member Function Documentation

int Ambertoppar::firstwat ( )

Definition at line 1096 of file parm.C.

References AtomNames, Ipres, Nres, and ResNames.

 {
         char    *restr = ResNames; 
         char    *lastres = ResNames + Nres * 4 + 1;
         int     res = 0;
 
         /*
          *  find 1st water residue
          */
 
         for (; restr<lastres; restr+=4) {
                 if (!strncmp(restr, "WAT ", 4)) {
                   printf("first water: res = %d, atom = %d (%.4s)\n", 
                                         res+1, Ipres[res],
                                         &AtomNames[Ipres[res]]);
 #ifndef NAMD_NO_STDOUT_FLUSH
                   fflush(stdout);
 #endif
                   return(Ipres[res]-1);
                 }
                 res++;
         }
         return(0);
 }

void Ambertoppar::genclose ( FILE * fileptr )

Definition at line 86 of file parm.C.

References Fclose().

Referenced by readparm().

 {
         Fclose(fileptr);
 }

FILE * Ambertoppar::genopen ( const char * name )

Definition at line 72 of file parm.C.

References Fopen().

Referenced by readparm().

 {
         return(Fopen(name,"r"));
 }

char * Ambertoppar::get ( int size )

Definition at line 96 of file parm.C.

References NAMD_die().

 {
         char    *ptr;
 
 #ifdef DEBUG
         printf("malloc %d\n", size);
 #ifndef NAMD_NO_STDOUT_FLUSH
         fflush(stdout);
 #endif
 #endif
         if (size ==0)
                 return((char *) NULL);
 
         if ((ptr = (char *) malloc((unsigned)size)) == NULL) {
                 printf("malloc %d", size);
 #ifndef NAMD_NO_STDOUT_FLUSH
                 fflush(stdout);
 #endif
                 NAMD_die("Memory allocation error in Ambertoppar::get()");
         }
         return(ptr);
 }

int Ambertoppar::moveto	(	FILE *	fp,
		const char *	label
	)

Definition at line 1226 of file parm.C.

References endi(), iout, iWARN(), and preadln().

Referenced by readparm().

 {
   char s[76],buf[81];
 
  while ( 1 ) {
   // Find the string "%FLAG"
   do preadln(fp, "parm file", buf);
   while (strncmp(buf,"%FLAG",5));
 
   // See if the label is what we expected
   sscanf(buf+5,"%s",s);
   if (strcasecmp(s,label))
     iout << iWARN << "Skipping " << s << " in parm file while seeking " << label << ".\n" << endi;
   else
     break;
  }
 
   // The next line should begin with "%FORMAT"
   preadln(fp, "parm file", buf);
   if (strncmp(buf,"%FORMAT",7))
     return 0;
 
   return 1;
 }

void Ambertoppar::preadln	(	FILE *	file,
		const char *	name,
		char *	string
	)

Definition at line 123 of file parm.C.

References NAMD_die().

Referenced by moveto(), and readparm().

 {
         int     i, j;
 
         for (i=0; i<81; i++) {
                 if ((j = getc(file)) == EOF) {
                         NAMD_die("Unexpected EOF in Amber parm file");
                         printf("Error: unexpected EOF in %s\n", name);
                 }
                 string[i] = (char) j;
                 if (string[i] == '\n') {
                         break;
                 }
         }
         if (i == 80  &&  string[i] != '\n') {
                 NAMD_die("Line too long in Amber parm file");
                 printf("Error: line too long in %s:\n%.80s", name, string);
         }
 }

int Ambertoppar::read_fortran_12I6	(	FILE *	fp,
		int *	data,
		int	count
	)

Definition at line 1201 of file parm.C.

References readtoeoln().

Referenced by readparm().

 {
   int i,j;
   char buf[7];
   
   for (i=0; i<count; ++i)
   { for (j=0; j<6; ++j)
     { buf[j]=getc(fp);
       if (buf[j]=='\n' || buf[j]=='\0' || buf[j]==EOF)
         return 0;
     }
     buf[6] = '\0';
     if (sscanf(buf,"%d",data+i) != 1)
       return 0;
     if (i%12==11 && i<count-1)
       readtoeoln(fp);
   }
   
   return 1;
 }

int Ambertoppar::readparm ( char * name )

Definition at line 151 of file parm.C.

References _REAL, AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Boundary, Charges, Cn1, Cn2, Cno, Cutcap, data_read, debug, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, endi(), ExclAt, genclose(), genopen(), HB12, HB6, Iac, Iblo, IfBox, IfCap, iout, Ipatm, Ipres, Iptres, ititl, Masses, Mbona, moveto(), Mphia, Mtheta, Nat3, Natcap, Natom, Natyp, Nbona, Nbonh, Nhparm, Nmxrs, Nnb, Nparm, Nphb, Nphia, Nphih, Nptra, Nres, Nspm, Nspsol, Ntheta, Ntheth, Nttyp, Ntype2d, Ntypes, Numang, Numbnd, Phase, Pk, Pn, preadln(), read_fortran_12I6(), readtoeoln(), Req, ResNames, Rk, Solty, Teq, Tk, TreeJoin, Xcap, Ycap, and Zcap.

Referenced by NamdState::loadStructure().

 {
         _REAL           *H;
         int             i, idum, res, ifpert;
         int             *buffer, amber7_format;
         FILE            *file;
 
         if (data_read)
         { iout << "Duplicate parm data in one object!\n" << endi;
           return(0);
         }
 
 //      printf("Reading parm file (%s)\n", name);
         iout << "Reading parm file (" << name << ") ...\n" << endi;
 
 //      if ((file = genopen(name, "parm")) == NULL) 
         if ((file = genopen(name)) == NULL)
                 return(0);
 
         /* READ TITLE */
 
         preadln(file, name, ititl);
 // "ititle" doesn't guarantee to have '\0' (as the end of a string),
 // so the following is disabled in order to avoid strange output
 //      printf("%s title:\n%s", name, ititl);
 
         // Check whether it's in AMBER 7 format or in old format
         
         if (strncmp(ititl,"%VERSION",8))
                 amber7_format = 0;  // old format
         else
         {       amber7_format = 1;  // AMBER 7 format
                 iout << "PARM file in AMBER 7 format\n" << endi;
                 if (!moveto(file,"TITLE"))
                 { genclose(file);
                   return 0;
                 }
                 preadln(file, name, ititl);
         }
 
         /* READ CONTROL INTEGERS */
 
         if (amber7_format)
         {       if (!moveto(file,"POINTERS"))
                 { genclose(file);
                   return 0;
                 }
 //      fscanf(file, f9118, 
                 fscanf(file, "%d%d%d%d%d%d%d%d%d%d%d%d",
                 &Natom,  &Ntypes, &Nbonh, &Mbona, 
                 &Ntheth, &Mtheta, &Nphih, &Mphia, 
                 &Nhparm, &Nparm,  &Nnb,   &Nres);
 
 //      fscanf(file, f9118, 
                 fscanf(file, "%d%d%d%d%d%d%d%d%d%d%d%d",
                 &Nbona,  &Ntheta, &Nphia, &Numbnd, 
                 &Numang, &Nptra,  &Natyp, &Nphb, 
                 &ifpert,      &idum,        &idum,       &idum);
 
                 fscanf(file, " %d %d %d %d %d %d", 
                 &idum, &idum,&idum,&IfBox,&Nmxrs,&IfCap);
         }
         else
         {       buffer = new int[30];
                 if (!read_fortran_12I6(file,buffer,30))
                 { genclose(file);
                   return 0;
                 }
                 Natom = buffer[0];
                 Ntypes = buffer[1];
                 Nbonh = buffer[2];
                 Mbona = buffer[3];
                 Ntheth = buffer[4];
                 Mtheta = buffer[5];
                 Nphih = buffer[6];
                 Mphia = buffer[7];
                 Nhparm = buffer[8];
                 Nparm = buffer[9];
                 Nnb = buffer[10];
                 Nres = buffer[11];
                 Nbona = buffer[12];
                 Ntheta = buffer[13];
                 Nphia = buffer[14];
                 Numbnd = buffer[15];
                 Numang = buffer[16];
                 Nptra = buffer[17];
                 Natyp = buffer[18];
                 Nphb = buffer[19];
                 ifpert = buffer[20];
                 IfBox = buffer[27];
                 Nmxrs = buffer[28];
                 IfCap = buffer[29];
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         if (ifpert) {
                 printf("not equipped to read perturbation prmtop\n");
                 return(0);
         }
 
         /* ALLOCATE MEMORY */
 
         Nat3 = 3 * Natom;
         Ntype2d = Ntypes * Ntypes;
         Nttyp = Ntypes*(Ntypes+1)/2;
 
         /*
          * get most of the indirect stuff; some extra allowed for char arrays
          */
 
         AtomNames = (char *) get(4*Natom+81);
         Charges = (_REAL *) get(sizeof(_REAL)*Natom);
         Masses = (_REAL *) get(sizeof(_REAL)*Natom);
         Iac = (int *) get(sizeof(int)*Natom);
         Iblo = (int *) get(sizeof(int)*Natom);
         Cno = (int *) get(sizeof(int)* Ntype2d);
         ResNames = (char *) get(4* Nres+81);
         Ipres = (int *) get(sizeof(int)*( Nres+1));
         Rk = (_REAL *) get(sizeof(_REAL)* Numbnd);
         Req = (_REAL *) get(sizeof(_REAL)* Numbnd);
         Tk = (_REAL *) get(sizeof(_REAL)* Numang);
         Teq = (_REAL *) get(sizeof(_REAL)* Numang);
         Pk = (_REAL *) get(sizeof(_REAL)* Nptra);
         Pn = (_REAL *) get(sizeof(_REAL)* Nptra);
         Phase = (_REAL *) get(sizeof(_REAL)* Nptra);
         Solty = (_REAL *) get(sizeof(_REAL)* Natyp);
         Cn1 = (_REAL *) get(sizeof(_REAL)* Nttyp);
         Cn2 = (_REAL *) get(sizeof(_REAL)* Nttyp);
         BondHAt1 = (int *) get(sizeof(int)* Nbonh);
         BondHAt2 = (int *) get(sizeof(int)* Nbonh);
         BondHNum = (int *) get(sizeof(int)* Nbonh);
         BondAt1 = (int *) get(sizeof(int)* Nbona);
         BondAt2 = (int *) get(sizeof(int)* Nbona);
         BondNum = (int *) get(sizeof(int)* Nbona);
         AngleHAt1 = (int *) get(sizeof(int)* Ntheth);
         AngleHAt2 = (int *) get(sizeof(int)* Ntheth);
         AngleHAt3 = (int *) get(sizeof(int)* Ntheth);
         AngleHNum = (int *) get(sizeof(int)* Ntheth);
         AngleAt1 = (int *) get(sizeof(int)* Ntheta);
         AngleAt2 = (int *) get(sizeof(int)*Ntheta);
         AngleAt3 = (int *) get(sizeof(int)*Ntheta);
         AngleNum = (int *) get(sizeof(int)*Ntheta);
         DihHAt1 = (int *) get(sizeof(int)*Nphih);
         DihHAt2 = (int *) get(sizeof(int)*Nphih);
         DihHAt3 = (int *) get(sizeof(int)*Nphih);
         DihHAt4 = (int *) get(sizeof(int)*Nphih);
         DihHNum = (int *) get(sizeof(int)*Nphih);
         DihAt1 = (int *) get(sizeof(int)*Nphia);
         DihAt2 = (int *) get(sizeof(int)*Nphia);
         DihAt3 = (int *) get(sizeof(int)*Nphia);
         DihAt4 = (int *) get(sizeof(int)*Nphia);
         DihNum = (int *) get(sizeof(int)*Nphia);
         ExclAt = (int *) get(sizeof(int)*Nnb);
         HB12 = (_REAL *) get(sizeof(_REAL)*Nphb);
         HB6 = (_REAL *) get(sizeof(_REAL)*Nphb);
         AtomSym = (char *) get(4*Natom+81);
         AtomTree = (char *) get(4*Natom+81);
         TreeJoin = (int *) get(sizeof(int)*Natom);
         AtomRes = (int *) get(sizeof(int)*Natom);
 
         /* 
          * READ ATOM NAMES -IH(M04)
          */
 
         if (amber7_format)
                 if (!moveto(file,"ATOM_NAME"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
                 preadln(file, "", &AtomNames[i*80]);
 
         /* 
          * READ ATOM CHARGES -X(L15)
          *      (pre-multiplied by an energy factor of 18.2223 == sqrt(332)
          *       for faster force field calculations)
          */
 
         if (amber7_format)
                 if (!moveto(file,"CHARGE"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<Natom; i++)
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Charges[i]);
 #else
                 fscanf(file, " %f", &Charges[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ ATOM MASSES -X(L20)
          */
 
         if (amber7_format)
                 if (!moveto(file,"MASS"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<Natom; i++)
 #ifdef DOUBLE
                 fscanf(file, " %le", &Masses[i]);
 #else
                 fscanf(file, " %e", &Masses[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ ATOM L-J TYPES -IX(I04)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"ATOM_TYPE_INDEX"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Natom; i++)
                         fscanf(file, " %d", &Iac[i]);
         }
         else
         {       if (!read_fortran_12I6(file,Iac,Natom))
                 { genclose(file);
                   return 0;
                 }
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ ATOM INDEX TO 1st IN EXCLUDED ATOM LIST "NATEX" -IX(I08)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"NUMBER_EXCLUDED_ATOMS"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Natom; i++)
                         fscanf(file, " %d", &Iblo[i]);
         }
         else
         {       if (!read_fortran_12I6(file,Iblo,Natom))
                 { genclose(file);
                   return 0;
                 }
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ TYPE INDEX TO N-B TYPE -IX(I06)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"NONBONDED_PARM_INDEX"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Ntype2d; i++)
                         fscanf(file, " %d", &Cno[i]);
         }
         else
         {       if (!read_fortran_12I6(file,Cno,Ntype2d))
                 { genclose(file);
                   return 0;
                 }
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ RES NAMES (4 chars each, 4th blank) -IH(M02)
          */
 
         if (amber7_format)
                 if (!moveto(file,"RESIDUE_LABEL"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<(Nres/20 + (Nres%20 ? 1 : 0)); i++)
                 preadln(file, "", &ResNames[i*80]);
 
         /* 
          * READ RES POINTERS TO 1st ATOM                -IX(I02)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"RESIDUE_POINTER"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nres; i++) 
                         fscanf(file, " %d", &Ipres[i]);
         }
         else
         {       if (!read_fortran_12I6(file,Ipres,Nres))
                 { genclose(file);
                   return 0;
                 }
 //      skipeoln(file);
                 readtoeoln(file);
         }
         Ipres[Nres] = Natom + 1;
 
         /* 
          * READ BOND FORCE CONSTANTS                    -RK()
          */
 
         if (amber7_format)
                 if (!moveto(file,"BOND_FORCE_CONSTANT"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Numbnd; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Rk[i]);
 #else
                 fscanf(file, " %f", &Rk[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ BOND LENGTH OF MINIMUM ENERGY           -REQ()
          */
 
         if (amber7_format)
                 if (!moveto(file,"BOND_EQUIL_VALUE"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Numbnd; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Req[i]);
 #else
                 fscanf(file, " %f", &Req[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ BOND ANGLE FORCE CONSTANTS (following Rk nomen) -TK()
          */
 
         if (amber7_format)
                 if (!moveto(file,"ANGLE_FORCE_CONSTANT"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Numang; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Tk[i]);
 #else
                 fscanf(file, " %f", &Tk[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ BOND ANGLE OF MINIMUM ENERGY (following Req nomen) -TEQ()
          */
 
         if (amber7_format)
                 if (!moveto(file,"ANGLE_EQUIL_VALUE"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Numang; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Teq[i]);
 #else
                 fscanf(file, " %f", &Teq[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ DIHEDRAL PEAK MAGNITUDE                 -PK()
          */
 
         if (amber7_format)
                 if (!moveto(file,"DIHEDRAL_FORCE_CONSTANT"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Nptra; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Pk[i]);
 #else
                 fscanf(file, " %f", &Pk[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ DIHEDRAL PERIODICITY                    -PN()
          */
 
         if (amber7_format)
                 if (!moveto(file,"DIHEDRAL_PERIODICITY"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Nptra; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Pn[i]);
 #else
                 fscanf(file, " %f", &Pn[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ DIHEDRAL PHASE                          -PHASE()
          */
 
         if (amber7_format)
                 if (!moveto(file,"DIHEDRAL_PHASE"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Nptra; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Phase[i]);
 #else
                 fscanf(file, " %f", &Phase[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * ?? "RESERVED"                                -SOLTY()
          */
 
         if (amber7_format)
                 if (!moveto(file,"SOLTY"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Natyp; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Solty[i]);
 #else
                 fscanf(file, " %f", &Solty[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ L-J R**12 FOR ALL PAIRS OF ATOM TYPES   -CN1()
          *      (SHOULD BE 0 WHERE H-BONDS)
          */
 
         if (amber7_format)
                 if (!moveto(file,"LENNARD_JONES_ACOEF"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Nttyp; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Cn1[i]);
 #else
                 fscanf(file, " %f", &Cn1[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ L-J R**6 FOR ALL PAIRS OF ATOM TYPES    -CN2()
          *      (SHOULD BE 0 WHERE H-BONDS)
          */
 
         if (amber7_format)
                 if (!moveto(file,"LENNARD_JONES_BCOEF"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i< Nttyp; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &Cn2[i]);
 #else
                 fscanf(file, " %f", &Cn2[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /* 
          * READ COVALENT BOND W/ HYDROGEN (3*(atnum-1)): 
          *      IBH = ATOM1             -IX(I12)
          *      JBH = ATOM2             -IX(I14)
          *      ICBH = BOND ARRAY PTR   -IX(I16)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"BONDS_INC_HYDROGEN"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nbonh; i++)
                         fscanf(file, " %d %d %d", 
                             &BondHAt1[i], &BondHAt2[i], &BondHNum[i]);
         }
         else
         {       buffer = new int[3*Nbonh];
                 if (!read_fortran_12I6(file,buffer,3*Nbonh))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nbonh; i++) 
                 { BondHAt1[i] = buffer[3*i];
                   BondHAt2[i] = buffer[3*i+1];
                   BondHNum[i] = buffer[3*i+2];
                 }
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ COVALENT BOND W/OUT HYDROGEN (3*(atnum-1)):
          *      IB = ATOM1              -IX(I18)
          *      JB = ATOM2              -IX(I20)
          *      ICB = BOND ARRAY PTR    -IX(I22)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"BONDS_WITHOUT_HYDROGEN"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nbona; i++)
                         fscanf(file, " %d %d %d", 
                                 &BondAt1[i], &BondAt2[i], &BondNum[i]);
         }
         else
         {       buffer = new int[3*Nbona];
                 if (!read_fortran_12I6(file,buffer,3*Nbona))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nbona; i++)
                 { BondAt1[i] = buffer[3*i];
                   BondAt2[i] = buffer[3*i+1];
                   BondNum[i] = buffer[3*i+2];
                 }
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ ANGLE W/ HYDROGEN: 
          *      ITH = ATOM1                     -IX(I24)
          *      JTH = ATOM2                     -IX(I26)
          *      KTH = ATOM3                     -IX(I28)
          *      ICTH = ANGLE ARRAY PTR          -IX(I30)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"ANGLES_INC_HYDROGEN"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Ntheth; i++)
                         fscanf(file, " %d %d %d %d", 
                                 &AngleHAt1[i], &AngleHAt2[i], 
                                 &AngleHAt3[i], &AngleHNum[i]);
         }
         else
         {       buffer = new int[4*Ntheth];
                 if (!read_fortran_12I6(file,buffer,4*Ntheth))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Ntheth; i++)
                 { AngleHAt1[i] = buffer[4*i];
                   AngleHAt2[i] = buffer[4*i+1];
                   AngleHAt3[i] = buffer[4*i+2];
                   AngleHNum[i] = buffer[4*i+3];
                 }
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ ANGLE W/OUT HYDROGEN: 
          *      IT = ATOM1                      -IX(I32)
          *      JT = ATOM2                      -IX(I34)
          *      KT = ATOM3                      -IX(I36)
          *      ICT = ANGLE ARRAY PTR           -IX(I38)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"ANGLES_WITHOUT_HYDROGEN"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Ntheta; i++)
                         fscanf(file, " %d %d %d %d", 
                                 &AngleAt1[i], &AngleAt2[i], 
                                 &AngleAt3[i], &AngleNum[i]);
         }
         else
         {       buffer = new int[4*Ntheta];
                 if (!read_fortran_12I6(file,buffer,4*Ntheta))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Ntheta; i++)
                 { AngleAt1[i] = buffer[4*i];
                   AngleAt2[i] = buffer[4*i+1];
                   AngleAt3[i] = buffer[4*i+2];
                   AngleNum[i] = buffer[4*i+3];
                 }
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ DIHEDRAL W/ HYDROGEN: 
          *      ITH = ATOM1                     -IX(40)
          *      JTH = ATOM2                     -IX(42)
          *      KTH = ATOM3                     -IX(44)
          *      LTH = ATOM4                     -IX(46)
          *      ICTH = DIHEDRAL ARRAY PTR       -IX(48)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"DIHEDRALS_INC_HYDROGEN"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nphih; i++)
                         fscanf(file, " %d %d %d %d %d", 
                                 &DihHAt1[i], &DihHAt2[i], &DihHAt3[i], 
                                 &DihHAt4[i], &DihHNum[i]);
         }
         else
         {       buffer = new int[5*Nphih];
                 if (!read_fortran_12I6(file,buffer,5*Nphih))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nphih; i++)
                 { DihHAt1[i] = buffer[5*i];
                   DihHAt2[i] = buffer[5*i+1];
                   DihHAt3[i] = buffer[5*i+2];
                   DihHAt4[i] = buffer[5*i+3];
                   DihHNum[i] = buffer[5*i+4];
                 }
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /* 
          * READ DIHEDRAL W/OUT HYDROGEN: 
          *      IT = ATOM1
          *      JT = ATOM2
          *      KT = ATOM3
          *      LT = ATOM4
          *      ICT = DIHEDRAL ARRAY PTR
          */
 
         if (amber7_format)
         {       if (!moveto(file,"DIHEDRALS_WITHOUT_HYDROGEN"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nphia; i++)
                         fscanf(file, " %d %d %d %d %d", 
                                 &DihAt1[i], &DihAt2[i], &DihAt3[i], 
                                 &DihAt4[i], &DihNum[i]);
         }
         else
         {       buffer = new int[5*Nphia];
                 if (!read_fortran_12I6(file,buffer,5*Nphia))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nphia; i++) {
                   DihAt1[i] = buffer[5*i];
                   DihAt2[i] = buffer[5*i+1];
                   DihAt3[i] = buffer[5*i+2];
                   DihAt4[i] = buffer[5*i+3];
                   DihNum[i] = buffer[5*i+4];
                 }
                 delete [] buffer;
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /*
          * READ EXCLUDED ATOM LIST      -IX(I10)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"EXCLUDED_ATOMS_LIST"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Nnb; i++)
                         fscanf(file, " %d", &ExclAt[i]);
         }
         else
         {       if (!read_fortran_12I6(file,ExclAt,Nnb))
                 { genclose(file);
                   return 0;
                 }
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /*
          * READ H-BOND R**12 TERM FOR ALL N-B TYPES     -ASOL()
          */
 
         if (amber7_format)
                 if (!moveto(file,"HBOND_ACOEF"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<Nphb; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &HB12[i]);
 #else
                 fscanf(file, " %f", &HB12[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /*
          * READ H-BOND R**6 TERM FOR ALL N-B TYPES      -BSOL()
          */
 
         if (amber7_format)
                 if (!moveto(file,"HBOND_BCOEF"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<Nphb; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &HB6[i]);
 #else
                 fscanf(file, " %f", &HB6[i]);
 #endif
 //      skipeoln(file);
         readtoeoln(file);
 
         /*
          * READ H-BOND CUTOFF (NOT USED) ??             -HBCUT()
          */
 
         if (amber7_format)
                 if (!moveto(file,"HBCUT"))
                 { genclose(file);
                   return 0;
                 }
         H = (_REAL *) get(Nphb * sizeof(_REAL));
         for (i=0; i<Nphb; i++) 
 #ifdef DOUBLE
                 fscanf(file, " %lf", &H[i]);
 #else
                 fscanf(file, " %f", &H[i]);
 #endif
         free((char *)H);
         
 //      skipeoln(file);
         readtoeoln(file);
 
         /*
          * READ ATOM SYMBOLS (FOR ANALYSIS PROGS)       -IH(M06)
          */
 
         if (amber7_format)
                 if (!moveto(file,"AMBER_ATOM_TYPE"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
                 preadln(file, "", &AtomSym[i*80]);
 
         /*
          * READ TREE SYMBOLS (FOR ANALYSIS PROGS)       -IH(M08)
          */
 
         if (amber7_format)
                 if (!moveto(file,"TREE_CHAIN_CLASSIFICATION"))
                 { genclose(file);
                   return 0;
                 }
         for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
                 preadln(file, "", &AtomTree[i*80]);
 
         /*
          * READ TREE JOIN INFO (FOR ANALYSIS PROGS)     -IX(I64)
          */
 
         if (amber7_format)
         {       if (!moveto(file,"JOIN_ARRAY"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Natom; i++)
                         fscanf(file, " %d", &TreeJoin[i]);
         }
         else
         {       if (!read_fortran_12I6(file,TreeJoin,Natom))
                 { genclose(file);
                   return 0;
                 }
 //      skipeoln(file);
                 readtoeoln(file);
         }
 
         /*
          * READ PER-ATOM RES NUMBER                     -IX(I66)
          *      NOTE: this appears to be something entirely different
          *      NOTE: overwriting this with correct PER-ATOM RES NUMBERs
          */
 
         if (amber7_format)
         {       if (!moveto(file,"IROTAT"))
                 { genclose(file);
                   return 0;
                 }
                 for (i=0; i<Natom; i++)
                         fscanf(file, " %d", &AtomRes[i]);
         }
         else
                 if (!read_fortran_12I6(file,AtomRes,Natom))
                 { genclose(file);
                   return 0;
                 }
         res = 0;
         for (i=0; i<Natom; i++) {
                 if (i+1 == Ipres[res+1])        /* atom is 1st of next res */
                         res++;
                 AtomRes[i] = res;
         }
       
         /*
          * BOUNDARY CONDITION STUFF
          */
 
         if (!IfBox) {
                 Nspm = 1;
                 Boundary = (int *) get(sizeof(int)*Nspm);
                 Boundary[0] = Natom;
         } else {
                 if (amber7_format)
                 {       if (!moveto(file,"SOLVENT_POINTERS"))
                         { genclose(file);
                           return 0;
                         }
                         fscanf(file, " %d %d %d", &Iptres, &Nspm, 
                                                         &Nspsol);
                 }
                 else
                 {
 //              skipeoln(file);
                         readtoeoln(file);
                         buffer = new int[3];
                         if (!read_fortran_12I6(file,buffer,3))
                         { genclose(file);
                           return 0;
                         }
                         Iptres = buffer[0];
                         Nspm = buffer[1];
                         Nspsol = buffer[2];
                         delete [] buffer;
 //              skipeoln(file);
                         readtoeoln(file);
                 }
                 Boundary = (int *) get(sizeof(int)*Nspm);
                 if (amber7_format)
                 {       if (!moveto(file,"ATOMS_PER_MOLECULE"))
                         { genclose(file);
                           return 0;
                         }
                         for (i=0; i<Nspm; i++)
                                 fscanf(file, " %d", &Boundary[i]);
                 }
                 else
                 {       if (!read_fortran_12I6(file,Boundary,Nspm))
                         { genclose(file);
                           return 0;
                         }
 //              skipeoln(file);
                         readtoeoln(file);
                 }
                 if (amber7_format)
                         if (!moveto(file,"BOX_DIMENSIONS"))
                         { genclose(file);
                           return 0;
                         }
 #ifdef DOUBLE
                 fscanf(file, " %lf %lf %lf", 
 #else
                 fscanf(file, " %f %f %f", 
 #endif
                                 &Box[0], &Box[1], &Box[2]);
 //              skipeoln(file);
                 readtoeoln(file);
                 if (Iptres)
                         Ipatm = Ipres[Iptres] - 1; 
                 /* IF(IPTRES.GT.0) IPTATM = IX(I02+IPTRES-1+1)-1 */
         }
 
         /*
          * ----- LOAD THE CAP INFORMATION IF NEEDED -----
          */
 
         // I don't know the label for it, so I don't read it if
         // it's AMBER 7 format. It's not used in NAMD anyway.
 //      if (IfCap) {
         if (IfCap && !amber7_format) {
                 /* if (IfBox) 
                         skipeoln(file); */
 #ifdef DOUBLE
                 fscanf(file, " %d %lf %lf %lf %lf", 
 #else
                 fscanf(file, " %d %f %f %f %f", 
 #endif
                                 &Natcap, &Cutcap, 
                                 &Xcap, &Ycap, &Zcap);
         }
         genclose(file);
         if (debug) {
                 printf("rdprm done\n");
 #ifndef NAMD_NO_STDOUT_FLUSH
                 fflush(stdout);
 #endif
         }
         data_read = 1;
         return(1);
 }